Security supervisor Illayaraaja Haridas, 29, student Gobi Nath Shanmugam, 21, and technician Tivanesvaran Sathivelu, 23, were accused of murdering Syed Kumar Yahya, 37, in Puchong -- a suburb of Kuala Lumpur -- three years ago.
Although the three men were initially charged separately, their cases were tried together as they involved the same victim.
In his closing argument, counsel Gobind Singh said none of the prosecution's witnesses or evidence could place his clients at the scene of the crime.
He added that the lack of a post mortem report amounted to a lack of evidence over how his clients were tied to the murder.
"It is clear cut that although my clients were in remand for three years, there was no case against them," Gobind told the court.
Deputy public prosecutor Muhamad Yasser Mohd Nasri said the medical report presented by the medical officer from Serdang Hospital, which deduced that the cause of death was severe head trauma, should be adequate.
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The prosecution argued that the three men's defence hung solely on their alibis.
Justice Ghazali Cha acquitted and discharged the three on the grounds that the prosecution had failed to prove a prima facie case against them.
"There was no evidence that they were present at the crime. None of the witnesses could identify the victim's attackers, which caused the fatal injuries which he succumbed to 10 days later," said Justice Ghazali.